Definitely not a dumb question. My method has evolved over the past year (it's hard to believe I built my first pedal little more than a year ago!). My first pedals were BYOC kits, so I simply cut the wire to the lengths as directed in the instructions. When I began to branch out, I adopted a "cut the wire the length of the enclosure" rule that I picked up reading tips here. Therefore:
Do you desolder the pots, trim the wires, then resolder?
Yes (kind of). Initially, I would test the circuit, remove the wire from the PCB (not from the pot, seems like less work. Also, usually not cutting, just heating and removing), and then cut to length once everything was in place. It occurred to me that if I had my enclosure drilled, etc. beforehand, I could save myself this step by measuring the length necessary for each run of wire from PCB to pot, jack, etc. However, I now have a completely different process. I test everything through my breadboard. I built a variation of a Beavis board
Here you can see I've gone back to the "length of the enclosure" rule for initial wire length. I tin the ends and run all the connections through the breadboard to a leftover stomp box. There are terminal strips for making connections to 9v, ground, in, out, and any pots/switches. And, if you think that's the end of it, you're wrong! I now don't bother mounting pots in the enclosure and instead keep a good number of PCB mounted pots of normal values that I can plug into the breadboard.
But in the end, there's always a "trim excess wire" step along the way!